You're standing on a caldera edge in Oia, Greek coffee in hand, looking at the blue dome of a church and thinking about your next stop. Mykonos. It’s right there, technically. On a map, the distance between these two Cycladic icons is roughly 64 nautical miles. You’d think a Santorini to Mykonos flight would be a breeze. A twenty-minute hop, right?
Not exactly.
Here is the cold, hard truth that most travel influencers gloss over while they’re busy editing their sunset reels: flying between these two islands is rarely a "straight shot." If you go looking for a direct commercial flight in 2026, you’re mostly going to find a giant headache involving a layover in Athens.
The Logistics of the Santorini to Mykonos Flight
Most people assume that because both islands have international airports—JTR in Santorini and JMK in Mykonos—there must be a shuttle plane. Nope. Because the ferry system is so dominant, major carriers like Aegean Airlines and Sky Express rarely find it profitable to run a "puddle jumper" between the two.
Instead, you’ll likely fly from Santorini (JTR) to Athens (ATH), sit in the terminal for two hours, and then board another plane to Mykonos (JMK).
It feels silly. It is silly.
You’re basically flying north to come back south. Total travel time? Usually 3 to 5 hours. Compare that to the high-speed ferry, which takes about 2 to 2.5 hours, and you start to see why the "flight" option is a bit of a niche choice.
Who actually flies this route?
- Point collectors: People using Star Alliance or other miles who want to keep their feet off a boat.
- The Seasick Crowd: Honestly, the Aegean Sea can get "choppy" is an understatement. When the Meltemi winds blow in July and August, those high-speed catamarans can feel like a mechanical bull. If your stomach can't handle the waves, the extra hours in the Athens airport are a small price to pay.
- The Private Jet Set: This is the only way to get a direct Santorini to Mykonos flight. If you have a few thousand Euros to burn, a private charter takes about 25 minutes.
The Athens Connection
If you are committed to the air, you’re going through Eleftherios Venizelos (ATH).
Don't book separate tickets. I can't stress this enough. If your first leg from Santorini is delayed by 20 minutes—which happens constantly because of the wind and the tiny, crowded tarmac at JTR—and you booked a separate ticket for the Mykonos leg, you are stuck. The airline won't help you.
Book it as a single itinerary.
Aegean Airlines is generally the gold standard here. Their "Olympic Air" subsidiary handles many of these domestic hops. The planes are usually ATR-72 turboprops or Airbus A320s. The turboprops are loud. They vibrate. Some people hate them, but they’re sturdy as hell in the Greek wind.
Baggage and the "Small Plane" Reality
The overhead bins on the smaller planes used for island hopping are microscopic. If you’re carrying a "standard" US-sized carry-on, expect to have it gate-checked. It’s not personal; it’s physics.
Also, watch the weight limits. European budget carriers like Volotea or Ryanair (who occasionally play in this space via Athens) will charge you more for an overweight bag than the cost of the actual seat.
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Comparing Costs: Flight vs. Ferry
Let's talk money.
A high-speed ferry (think SeaJets or Blue Star) usually runs between 60€ and 90€ for a one-way trip.
A Santorini to Mykonos flight via Athens? You're looking at anywhere from 120€ to 350€ depending on how far in advance you book. If you’re booking last minute in August, God help your wallet.
- Last Minute: Flying is almost always double the price of the boat.
- Comfort: The business lounge in Athens is great. The "lounge" at the Santorini port is basically a hot room filled with 500 sweaty people and a lot of suitcases.
- Reliability: Ferries get cancelled when the wind hits 7 or 8 on the Beaufort scale. Planes usually keep flying unless it’s a literal gale.
The Private Charter Loophole
I mentioned this earlier, but it’s worth a deeper look if you’re traveling in a group of four or more. Companies like BlueVelo or Greek Air Taxi Network operate light aircraft and helicopters.
A helicopter transfer is the ultimate "I’ve arrived" move. It’s also the only way to get that direct flight. It’s expensive—think 2,500€ to 4,000€ for the whole bird—but if you split it between six people, it’s still pricey, but significantly faster. Plus, the view of the Cyclades from 5,000 feet is something you won't forget. You see the circular shape of the Santorini caldera in a way no boat passenger ever will.
Seasonal Fluctuations
The "season" in Greece is widening. It used to be June to September. Now, it’s April to November.
During the winter (December through March), the Santorini to Mykonos flight options dwindle to almost nothing. The ferries are also sparse. Mykonos basically goes to sleep in the winter. If you're trying to do this trip in January, you must fly through Athens, and you might find only one flight a day that connects reasonably.
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The Airport Experience in Santorini (JTR)
JTR has been renovated recently by Fraport, so it’s much better than the third-world shed it used to be. But it’s still small.
Don't show up three hours early. You’ll just be standing around. Ninety minutes is usually the sweet spot. The security line can look long, but it moves fast. The real bottleneck is the gate area. There isn't enough seating for three departing flights at once, so prepare to stand or sit on your suitcase.
Arriving in Mykonos (JMK)
When you land in Mykonos, the chaos begins.
The airport is about 4km from the town center. Taxis are notoriously difficult to find in Mykonos—there are only about 30-50 taxis for the whole island. Most hotels offer a shuttle. Use it. If your hotel doesn't offer one, pre-book a private transfer. Walking from the airport to town is not an option; there are no sidewalks and the drivers are... assertive.
Common Misconceptions
People think flying saves time.
It doesn't.
By the time you get to the Santorini airport (30 mins), wait (90 mins), fly to Athens (45 mins), layover (90 mins), and fly to Mykonos (45 mins), you’ve spent your entire day. The ferry is a "center-to-center" transfer. You go from the port to the port.
However, flying is "cleaner." No salt spray, no sea sickness, no luggage-hauling onto a ramp while a crewman yells "Gogogogo!" in Greek.
Actionable Steps for Your Trip
If you’re dead set on taking a Santorini to Mykonos flight, follow this sequence to avoid the common pitfalls:
- Check the Ferry Schedule First: Visit FerryHopper or DirectFerries. If the wind forecast is under 20 mph, the boat is probably your best bet.
- Search Multi-City Flights: Use a meta-search engine like Google Flights or Skyscanner, but always navigate to the airline's direct website (Aegean/Olympic) to finalize the booking. This makes rebooking easier if a delay occurs.
- Buffer Your Layovers: Ensure you have at least 90 minutes in Athens. While ATH is an efficient airport, a 45-minute connection is gambling with your luggage's life.
- Consider the "Open Jaw" Ticket: If you haven't booked your international flights yet, fly into Santorini and out of Mykonos (or vice-versa). This eliminates the need to backtrack or do a mid-trip transfer entirely.
- Download the Aegean App: It’s actually quite good. You’ll get real-time gate change alerts, which are frequent in the chaotic Greek summer schedule.
- Pack a Light Jacket: Even if it’s 90°F in Fira, the air conditioning in the Athens airport and on the planes is set to "arctic."
Ultimately, the choice between the air and the sea comes down to your tolerance for waves versus your tolerance for layovers. The direct Santorini to Mykonos flight remains the white whale of Greek travel—often talked about, but rarely seen in the wild without a private pilot's license. Plan for the Athens stopover, enjoy a quick souvlaki in the terminal, and you'll get to the Mykonos beach clubs eventually.